PROSITE documentation PDOC50164GIY-YIG domain profile
Nucleases of the GIY-YIG family are involved in many cellular processes, including DNA repair and recombination, transfer of mobile genetic elements, and restriction of incoming foreign DNA. The GIY-YIG superfamily groups together nucleases characterized by the presence of a domain of typically ~100 amino acids, with two short motifs "GIY" and "YIG" in the N-terminal part, followed by an Arg residue in the center and a Glu residue in the C-terminal part [1,2,3,4,5].
The GIY-YIG domain forms a compact structural domain, which serves as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. The GIY-YIG domain has an α/β-sandwich architecture with a central three-stranded antiparallel β-sheet flanked by three-helices (see <PDB:1MK0>). The three-stranded anti-parallel β-sheet contains the GIY-YIG sequence elements. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site [2,3,4,5].
Some proteins known to contain a GIY-YIG domain are listed below:
- Eukaryotic Slx-1 proteins, involved in the maintenance of the rDNA copy number. They have a C-terminal RING finger Zn-binding domain (see <PDOC00449>).
- Mamalian ankyrin repeat (see <PDOC50088>) and LEM (see <PDOC50954>) domain- containing protein 1 (ANKLE1).
- Bacterial and archaeal UvrC subunits of (A)BC excinucleases, which remove damaged nucleotides by incising the damaged strand on both sides of the lesion.
- Paramecium bursaria Chlorella virus 1 (pbvc1).
- Phage T4 endonucleases SegA to E, probably involved in the movement of the endonuclease-encoding DNA.
- Phage T4 intron-associated endonuclease 1 (I-TevI), specific to the thymidylate synthase (td) gene splice junction and involved in intron homing.
The profile we developed covers the entire GIY-YIG domain.
Last update:May 2012 / Profile and text revised.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Kowalski J.C. Belfort M. Stapleton M.A. Holpert M. Dansereau J.T. Pietrokovski S. Baxter S.M. Derbyshire V. |
| Title | Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. | |
| Source | Nucleic Acids Res. 27:2115-2125(1999). | |
| PubMed ID | 10219084 |
| 2 | Authors | Van Roey P. Meehan L. Kowalski J.C. Belfort M. Derbyshire V. |
| Title | Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. | |
| Source | Nat. Struct. Biol. 9:806-811(2002). | |
| PubMed ID | 12379841 | |
| DOI | 10.1038/nsb853 |
| 3 | Authors | Truglio J.J. Rhau B. Croteau D.L. Wang L. Skorvaga M. Karakas E. DellaVecchia M.J. Wang H. Van Houten B. Kisker C. |
| Title | Structural insights into the first incision reaction during nucleotide excision repair. | |
| Source | EMBO J. 24:885-894(2005). | |
| PubMed ID | 15692561 | |
| DOI | 10.1038/sj.emboj.7600568 |
| 4 | Authors | Dunin-Horkawicz S. Feder M. Bujnicki J.M. |
| Title | Phylogenomic analysis of the GIY-YIG nuclease superfamily. | |
| Source | BMC Genomics 7:98-98(2006). | |
| PubMed ID | 16646971 | |
| DOI | 10.1186/1471-2164-7-98 |
| 5 | Authors | Ibryashkina E.M. Sasnauskas G. Solonin A.S. Zakharova M.V. Siksnys V. |
| Title | Oligomeric structure diversity within the GIY-YIG nuclease family. | |
| Source | J. Mol. Biol. 387:10-16(2009). | |
| PubMed ID | 19361436 | |
| DOI | 10.1016/j.jmb.2009.01.048 |
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